[phenixbb] More stringent water picking
Pavel Afonine
pafonine at lbl.gov
Mon Mar 19 10:01:57 PDT 2007
Hi Carsten,
thanks for your question!
The main water picking criteria in phenix.refine are:
1) Fo-Fc map;
2) 2Fo-Fc map;
3) macromolecule - water distance;
4) water-water distance;
5) B-factors and occupancies max/min values;
plus some more of expert level ...
There is no specific H-bonding criteria implemented. You can play with
sigma cutoff for both maps and with the distances above. In most of the
cases it the reasonable behavior.
I would be interested in Paul's (Adams) comments about his experience of
usefulness of H-bonding criteria in CNS.
Thanks!
Pavel.
Schubert, Carsten [PRDUS] wrote:
>
> Hi,
>
> is it possible to increase the stringency criteria for picked waters,
> besides increasing the sigma level? E.G. something on the order of the
> H-bonding criterion found in CNS? I find that the automated
> water-picking routine gives me quite a few waters, which are not
> necessarily justified by visual inspection of the maps.
>
> Thanks
>
> Carsten
>
>
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